An automatic system of patient alignment is required in order to monitor changes that occur in the period between magnetic resonance scans. For each scan of the patient a prime requisite is to register the images with respect to each other. The orthogonal relationship between the sagittal and transverse images should, in principle, identify a single common line at the intersection of the two image planes. The basis of the comparison requires spatial registration of the two images to correct for the probable translational and rotational tilts as well as for the geometrical and intensity distortions. This paper describes a number of automatic techniques which compare, pixel-by-pixel, first two synthetic images, and then their application to real images obtained separately from the same head and neck object field. The robustness, computational cost and effectiveness of the techniques presented are discussed, and computed results on real data for the most promising technique based on the Ratio Absolute Difference algorithm are presented.